words_probabilities {drimmR}

Probability of appearance of several words at several positions of a DMM

Description

Probability of appearance of several words at several positions of a DMM

Usage

words_probabilities(words, pos, x, output_file = NULL, plot = FALSE)

Arguments

words

A vector of characters containing words

pos

A vector of integer positions

x

An object of class dmm

output_file

(Optional) A file containing the matrix of probabilities (e.g,"C:/.../PROB.txt")

plot

FALSE (default); TRUE (display figure plots of words' probabilities by position)

Value

A dataframe of word probabilities along the positions of the sequence

Author(s)

Victor Mataigne, Alexandre Seiller

References

Barbu VS, Vergne N (2018). “Reliability and survival analysis for drifting Markov models: modelling and estimation.” Methodology and Computing in Applied Probability, 1–33. doi: 10.1007/s11009-018-9682-8, https://doi.org/10.1007/s11009-018-9682-8. Vergne N (2008). “Drifting Markov models with polynomial drift and applications to DNA sequences.” Statistical Applications in Genetics Molecular Biology , 7(1) . doi: 10.2202/1544-6115.1326, https://doi.org/10.2202/1544-6115.1326.

See Also

fitdmm, getTransitionMatrix, word_probability, word_probabilities

Examples

data(lambda, package = "drimmR")
dmm <- fitdmm(lambda, 1, 1, c('a','c','g','t'), init.estim = "freq",
fit.method="sum")
words <- c("atcgattc", "taggct", "ggatcgg")
pos <- c(100,300)
words_probabilities(words=words,pos=pos,dmm,plot=TRUE)